Patents by Inventor John E. P. Syka
John E. P. Syka has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Methods for mass spectrometry of mixtures of proteins or polypeptides using proton transfer reaction
Patent number: 10497549Abstract: A method comprises: (1) making an extract of a biological sample; (2) repeatedly: (a) choosing a respective one of a plurality of pre-determined protein or polypeptide analyte compounds; (b) introducing a portion of the extract into an electrospray ionization source, thereby generating positive ions comprising a plurality of ion species; (c) isolating a plurality of subsets of the ion species comprising respective mass-to-charge (m/z) ratio ranges, each range including an m/z ratio corresponding to a respective protonation state of the chosen compound; (d) reacting the isolated plurality of subsets of first-generation ion species with proton transfer reaction reagent anions for a pre-determined time duration; (e) generating a mass spectrum of the product ion species; and (g) identifying either the presence or absence of the compound based on the mass spectrum; and (3) identifying the presence or absence of the microorganism within the sample based on analytes present.Type: GrantFiled: December 4, 2017Date of Patent: December 3, 2019Assignee: THERMO FINNIGAN LLCInventors: James L. Stephenson, Jr., John E. P. Syka, August A. Specht -
Patent number: 10424475Abstract: A method of operating an electrostatic trapping mass analyzer, comprising: introducing a sample of ions into a trapping region of the mass analyzer, wherein a trapping field within the trapping region is such that the ions exhibit radial motion with respect to a central longitudinal axis of the trapping region while undergoing harmonic motion in a dimension defined by the central longitudinal axis, the frequency of harmonic motion of a particular ion being a function of its mass-to-charge ratio; superimposing a modulation field onto the trapping field within the trapping region, the modulation field acting to either increase or reduce the harmonic motion energies of the ions by an amount varying according to the frequency of harmonic motion; and acquiring a mass spectrum of the ions in the trapping region by measuring a signal representative of an image current induced by the harmonic motion of the ions.Type: GrantFiled: December 17, 2018Date of Patent: September 24, 2019Assignee: THERMO FINNIGAN LLCInventors: Chad R. Weisbrod, Michael W. Senko, Jesse D. Canterbury, John E. P. Syka
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Publication number: 20190122879Abstract: A method of operating an electrostatic trapping mass analyzer, comprising: introducing a sample of ions into a trapping region of the mass analyzer, wherein a trapping field within the trapping region is such that the ions exhibit radial motion with respect to a central longitudinal axis of the trapping region while undergoing harmonic motion in a dimension defined by the central longitudinal axis, the frequency of harmonic motion of a particular ion being a function of its mass-to-charge ratio; superimposing a modulation field onto the trapping field within the trapping region, the modulation field acting to either increase or reduce the harmonic motion energies of the ions by an amount varying according to the frequency of harmonic motion; and acquiring a mass spectrum of the ions in the trapping region by measuring a signal representative of an image current induced by the harmonic motion of the ions.Type: ApplicationFiled: December 17, 2018Publication date: April 25, 2019Inventors: Chad R. WEISBROD, Michael W. SENKO, Jesse D. CANTERBURY, John E. P. SYKA
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Publication number: 20190072566Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) and real-time data analysis methods are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: ApplicationFiled: November 7, 2018Publication date: March 7, 2019Inventors: Ping F. YIP, James L. STEPHENSON, JR., John E. P. SYKA
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Patent number: 10192730Abstract: A method of operating an electrostatic trapping mass analyzer, comprising: introducing a sample of ions into a trapping region of the mass analyzer, wherein a trapping field within the trapping region is such that the ions exhibit radial motion with respect to a central longitudinal axis of the trapping region while undergoing harmonic motion in a dimension defined by the central longitudinal axis, the frequency of harmonic motion of a particular ion being a function of its mass-to-charge ratio; superimposing a modulation field onto the trapping field within the trapping region, the modulation field acting to either increase or reduce the harmonic motion energies of the ions by an amount varying according to the frequency of harmonic motion; and acquiring a mass spectrum of the ions in the trapping region by measuring a signal representative of an image current induced by the harmonic motion of the ions.Type: GrantFiled: August 30, 2016Date of Patent: January 29, 2019Assignee: Thermo Finnigan LLCInventors: Chad R. Weisbrod, Michael W. Senko, Jesse D. Canterbury, John E. P. Syka
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Patent number: 10151758Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) and real-time data analysis methods are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: GrantFiled: January 13, 2017Date of Patent: December 11, 2018Assignee: THERMO FINNIGAN LLCInventors: Ping F. Yip, James L. Stephenson, Jr., John E. P. Syka
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Publication number: 20180323050Abstract: A method for operating a mass spectrometer comprises: generating a stream of ions by an ion source; directing the stream of ions into a first one of a pair of ion storage locations and trapping a first portion of the ions therein; directing a packet of ions from the other one of the pair of ion storage locations into an ion cooling cell that damps the kinetic energy of the ions comprising the packet of ions; directing the packet of ions to a mass analyzer of the mass spectrometer for mass analysis thereby; directing the first portion of ions from the first one of the pair of ion storage locations into the ion cooling cell; and directing the first portion of ions to the mass analyzer for mass analysis thereby.Type: ApplicationFiled: May 5, 2017Publication date: November 8, 2018Inventors: Johnathan Wayne SMITH, John E. P. SYKA
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Patent number: 9991107Abstract: A method is described that produces product ions for mass analysis, the method comprising the steps of: introducing precursor ions into an RF electric field ion containment device, introducing reagent ions into the RF electric field ion containment device and performing an ion-ion interaction in the RF electric field ion containment device by co-trapping the precursor ions with the reagent ions. Precursor ions and product ions may be retained and/or isolated in the RF electric field ion containment device. The steps above may be repeated until a predetermined amount of reaction completeness is attained. Mass analysis of at least some of the ions in the RF electric field ion containment device may be performed where the ions are mass analyzed either directly from the RF electric field ion containment device.Type: GrantFiled: June 21, 2016Date of Patent: June 5, 2018Assignee: Thermo Finnigan LLCInventors: Christopher Mullen, Chad R. Weisbrod, John E. P. Syka
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Publication number: 20180102243Abstract: A method comprises: (1) making an extract of a biological sample; (2) repeatedly: (a) choosing a respective one of a plurality of pre-determined protein or polypeptide analyte compounds; (b) introducing a portion of the extract into an electrospray ionization source, thereby generating positive ions comprising a plurality of ion species; (c) isolating a plurality of subsets of the ion species comprising respective mass-to-charge (m/z) ratio ranges, each range including an m/z ratio corresponding to a respective protonation state of the chosen compound; (d) reacting the isolated plurality of subsets of first-generation ion species with proton transfer reaction reagent anions for a pre-determined time duration; (e) generating a mass spectrum of the product ion species; and (g) identifying either the presence or absence of the compound based on the mass spectrum; and (3) identifying the presence or absence of the microorganism within the sample based on analytes present.Type: ApplicationFiled: December 4, 2017Publication date: April 12, 2018Inventors: James L. STEPHENSON, JR., John E. P. SYKA, August A. SPECHT
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Publication number: 20180061625Abstract: A method of operating an electrostatic trapping mass analyzer, comprising: introducing a sample of ions into a trapping region of the mass analyzer, wherein a trapping field within the trapping region is such that the ions exhibit radial motion with respect to a central longitudinal axis of the trapping region while undergoing harmonic motion in a dimension defined by the central longitudinal axis, the frequency of harmonic motion of a particular ion being a function of its mass-to-charge ratio; superimposing a modulation field onto the trapping field within the trapping region, the modulation field acting to either increase or reduce the harmonic motion energies of the ions by an amount varying according to the frequency of harmonic motion; and acquiring a mass spectrum of the ions in the trapping region by measuring a signal representative of an image current induced by the harmonic motion of the ions.Type: ApplicationFiled: August 30, 2016Publication date: March 1, 2018Inventors: Chad R. WEISBROD, Michael W. SENKO, Jesse D. CANTERBURY, John E. P. SYKA
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Publication number: 20170365453Abstract: A method is described that produces product ions for mass analysis, the method comprising the steps of: introducing precursor ions into an RF electric field ion containment device, introducing reagent ions into the RF electric field ion containment device and performing an ion-ion interaction in the RF electric field ion containment device by co-trapping the precursor ions with the reagent ions. Precursor ions and product ions may be retained and/or isolated in the RF electric field ion containment device. The steps above may be repeated until a predetermined amount of reaction completeness is attained. Mass analysis of at least some of the ions in the RF electric field ion containment device may be performed where the ions are mass analyzed either directly from the RF electric field ion containment device.Type: ApplicationFiled: June 21, 2016Publication date: December 21, 2017Inventors: Christopher MULLEN, Chad R. WEISBROD, John E. P. SYKA
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Patent number: 9837255Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: GrantFiled: July 17, 2015Date of Patent: December 5, 2017Assignee: Thermo Finnigan LLCInventors: James L. Stephenson, Jr., John E. P. Syka, August A. Specht
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Publication number: 20170205425Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) and real-time data analysis methods are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: ApplicationFiled: January 13, 2017Publication date: July 20, 2017Inventors: Ping F. YIP, James L. STEPHENSON, JR., John E. P. SYKA
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Patent number: 9711340Abstract: A method of aligning a light beam within a mass spectrometer includes providing precursor ions along a longitudinal axis of the mass spectrometer at two or more precursor ion locations, the precursor ion locations being spatially separated along the longitudinal axis of the mass spectrometer, the precursor ions forming in-vacuum targets. The method then includes directing a light beam from a light source in a direction along the longitudinal axis of the mass spectrometer, the light beam photo-dissociating the precursor ions, and monitoring a mass spectrometer ion signal from each of the two or more precursor ion locations while adjusting the direction of the light beam, thereby aligning the light beam within the mass spectrometer.Type: GrantFiled: May 26, 2016Date of Patent: July 18, 2017Assignee: Thermo Finnigan LLCInventors: Chad R. Weisbrod, Christopher Mullen, John E. P. Syka, Jae C. Schwartz
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Publication number: 20170162372Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: ApplicationFiled: July 17, 2015Publication date: June 8, 2017Applicant: Thermo Finnigan LLCInventors: James L. STEPHENSON, Jr., John E. P. SYKA, August A. SPECHT
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Publication number: 20160358766Abstract: A method and apparatus are disclosed for dissociation of precursor ions, such as polypeptides, by ultraviolet photodissociation (UVPD) for mass spectrometry analysis. Precursor ions are confined within an ion trap and irradiated with ultraviolet (UV) light, which may take the form of pulses emitted by a laser. The precursor ions absorb the UV light and dissociate into product ions. To avoid the condition of overfragmentation arising from further dissociation of the product ions, an excitation field is established within the ion trap such that the product ions, but not the precursor ions, are kinetically excited to trajectories that extend outside of the irradiated region.Type: ApplicationFiled: June 2, 2016Publication date: December 8, 2016Inventors: Chad R. WEISBROD, Jae C. SCHWARTZ, John E. P. SYKA
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Patent number: 9171707Abstract: The invention provides improvements in reagents for use in electron transfer dissociation ionization techniques for use in mass spectrometry, particularly for sequencing peptides and proteins using mass spectrometric techniques involving electrospray ionization and MS/MS characterization of fragment ions. The novel reagents used in the inventive methods allow for more effective determination of protein sequences, especially of long peptides or post-translationally modified protein fragments. Use of the polycyclic aromatic hydrocarbons azulene, homoazulene, and acenaphthylene, and homodimers and heterodimers thereof, are described.Type: GrantFiled: September 2, 2010Date of Patent: October 27, 2015Assignee: University of Virginia Patent FoundationInventors: John E. P. Syka, Philip D. Compton, Donald F. Hunt
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Patent number: 9159542Abstract: An ion source apparatus for a mass spectrometer comprises a refractory metal filament operable to provide a flow of electrons by thermionic emission; an electrical current source electrically coupled to the filament for heating the filament; a vacuum chamber enclosing the filament; an ionization volume within the vacuum chamber capable of receiving the flow of electrons; a source of an oxygen-providing gas or gases; a restrictive fluidic coupling to the source of oxygen-providing gas or gases; and a gas conduit fluidically coupled to the restrictive fluidic coupling, the restrictive fluidic coupling and conduit operable to provide a flow of the oxygen-providing gas or gases into the vacuum chamber so as to maintain a partial pressure of said gas or gases within the vacuum chamber that is sufficiently high so as to inhibit the otherwise formation of a carbonaceous growth on the filament in the presence of a gaseous carbon-containing material.Type: GrantFiled: February 17, 2012Date of Patent: October 13, 2015Assignee: Thermo Finnigan LLCInventors: Christopher Mullen, John E. P. Syka, Scott T. Quarmby
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Publication number: 20130214147Abstract: An ion source apparatus for a mass spectrometer comprises a refractory metal filament operable to provide a flow of electrons by thermionic emission; an electrical current source electrically coupled to the filament for heating the filament; a vacuum chamber enclosing the filament; an ionization volume within the vacuum chamber capable of receiving the flow of electrons; a source of an oxygen-providing gas or gases; a restrictive fluidic coupling to the source of oxygen-providing gas or gases; and a gas conduit fluidically coupled to the restrictive fluidic coupling, the restrictive fluidic coupling and conduit operable to provide a flow of the oxygen-providing gas or gases into the vacuum chamber so as to maintain a partial pressure of said gas or gases within the vacuum chamber that is sufficiently high so as to inhibit the otherwise formation of a carbonaceous growth on the filament in the presence of a gaseous carbon-containing material.Type: ApplicationFiled: February 17, 2012Publication date: August 22, 2013Inventors: Christopher MULLEN, John E. P. SYKA, Scott T. QUARMBY
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Publication number: 20120156792Abstract: The invention provides improvements in reagents for use in electron transfer dissociation ionization techniques for use in mass spectrometry, particularly for sequencing peptides and proteins using mass spectrometric techniques involving electro-spray ionization and MS/MS characterization of fragment ions. The novel reagents used in the inventive methods allow for more effective determination of protein sequences, especially of long peptides or post-translationally modified protein fragments. Use of the polycyclic aromatic hydrocarbons azulene, homoazulene, and acenaphthylene, and homodimers and heterodimers thereof, are described.Type: ApplicationFiled: September 2, 2010Publication date: June 21, 2012Applicant: University of Virginia Patent FoundationInventors: John E.P. Syka, Philip D. Compton, Donald F. Hunt